GNPS analysis throwing non-finite values error

[mita0000]

Certain combinations of case/control groups throw the error below:

RuntimeError: The data contains non-finite values.
Traceback:
File "/home/jw247a/.local/share/virtualenvs/PALS-fesh4CcU/lib/python3.8/site-packages/streamlit/script_runner.py", line 333, in _run_script
exec(code, module.dict)
File "/home/jw247a/PALS/pals/run_gui.py", line 165, in
main()
File "/home/jw247a/PALS/pals/run_gui.py", line 78, in main
results = run_analysis(params)
File "/home/jw247a/.local/share/virtualenvs/PALS-fesh4CcU/lib/python3.8/site-packages/streamlit/caching.py", line 603, in wrapped_func
return get_or_create_cached_value()
File "/home/jw247a/.local/share/virtualenvs/PALS-fesh4CcU/lib/python3.8/site-packages/streamlit/caching.py", line 587, in get_or_create_cached_value
return_value = func(*args, **kwargs)
File "./pals/run_gui_gnps.py", line 78, in run_analysis
df = PLAGE_decomposition(ds)
File "/home/jw247a/.local/share/virtualenvs/PALS-fesh4CcU/lib/python3.8/site-packages/streamlit/caching.py", line 603, in wrapped_func
return get_or_create_cached_value()
File "/home/jw247a/.local/share/virtualenvs/PALS-fesh4CcU/lib/python3.8/site-packages/streamlit/caching.py", line 585, in get_or_create_cached_value
return_value = func(*args, **kwargs)
File "./pals/run_gui_gnps.py", line 126, in PLAGE_decomposition
df = method.get_results()
File "./pals/PLAGE.py", line 71, in get_results
plage_df = self.set_up_resample_plage_p_df(activity_df, streamlit_pbar=streamlit_pbar)
File "./pals/PLAGE.py", line 125, in set_up_resample_plage_p_df
pvalues = self._compare_resamples(tvalues, null_max_tvalues, null_min_tvalues)
File "./pals/PLAGE.py", line 334, in _compare_resamples
maxparams = genextreme.fit(null_max_tvalues)
File "/home/jw247a/.local/share/virtualenvs/PALS-fesh4CcU/lib/python3.8/site-packages/scipy/stats/_distn_infrastructure.py", line 2378, in fit
raise RuntimeError("The data contains non-finite values.")

The GNPS link: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=40e3f11e31ad4f319497f9f4e47c2e47
The metadata file is attached below. It doesn't seem to be a metadata file issue--is it because of the GNPS data?

Thank you!
metadata_iBAT.csv

[joewandy]

Thanks for reporting the issue above.

I tested with the GNPS link above and also managed to reproduce the error with
Control: iBat_Wildling_Chow
Case: iBat_Lab_HFCDD

It seems that this is caused by certain molecular familiar having the same member MS1 intensity values throughout the case and/or control groups. This causes the within-group variance to be zero, so the t-statistic during permutation test becomes undefined (NaN), which breaks the codes. As a fix, I've excluded those MFs from calculation. They'd still appear in the final results but right at the bottom with p-values of 1.0, and can be ignored. Hope that helps. Any other problem, please let me know.

Joe